diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java index aef18d6a2..df74f8938 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java @@ -138,10 +138,14 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter { Map genotypeMap = genotypeListToSampleNameMap(genotypes); + // keep track of the total read depth + int totalReadDepth = 0; + for (String name : mHeader.getGenotypeSamples()) { if (genotypeMap.containsKey(name)) { Genotype gtype = genotypeMap.get(name); VCFGenotypeRecord record = createVCFGenotypeRecord(params, (VCFGenotypeCall)gtype); + totalReadDepth += ((VCFGenotypeCall)gtype).getReadCount(); params.addGenotypeRecord(record); genotypeMap.remove(name); } else { @@ -157,6 +161,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter { } Map infoFields = getInfoFields((VCFGenotypeLocusData)locusdata, params); + infoFields.put("DP", String.format("%d", totalReadDepth)); double qual = (locusdata == null) ? 0 : ((VCFGenotypeLocusData)locusdata).getConfidence(); // maintain 0-99 based Q-scores diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 9ad9adf09..8f1495ad0 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1, - Arrays.asList("9985a92060b512b5d27b4074faf8b60b")); + Arrays.asList("4f14792e79adef415efaf97e946460e3")); executeTest("testMultiSamplePilot1", spec); } @@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 50", 1, - Arrays.asList("394f009c9bad34eb584fa10d133d79e0")); + Arrays.asList("e3a701fd5f1fe4a84746f17ad4b3b3c3")); executeTest("testMultiSamplePilot2", spec); }